[gmx-users] free energy and fatal error
mgoette at mpi-bpc.mpg.de
Mon Jun 26 12:12:49 CEST 2006
Are those atoms mentioned, perturbed ones?
I think, it has nothing to do with the error, you experience, but
delta_lambda should be 1/number of steps, if you want to do TI from 0 to 1.
Anyway, maybe you should look at the energies on these atoms and perhaps
recheck your bonded parameters...
More details, like your mdp-file, would be helpful.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
MURAT CETINKAYA wrote:
> I am trying to calculate solvation free energy of a non-standard residue and I
> have problems in vacuum runs.
> I defined a dummy atom for every single atom in the molecule (0 charge and
> non-bonded parameters) and I input every single bonded interaction values
> manually (in order to prevent any errors resulting from that).
> I minimized my molecule with l-bfgs and steep. If do free energy = no, I can do
> my NVT run in vacuo without any problems. However, when I set:
> free_energy = yes
> init_lambda = 0.0
> delta_lambda = 0
> sc_alpha = 0.5
> sc-power = 1.0
> sc-sigma = 0.3
> I get the following error:
> step 0Warning: 1-4 interaction between 21 and 23 at distance larger than 2.4 nm
> These are ignored for the rest of the simulation
> turn on -debug for more information
> Fatal error: ci = -2147483648 should be in 0 .. 63 [FILE nsgrid.c, LINE 218]
> As I said, every bonded interaction value is entered manually (A = B values) and
> structure seems minimized.
> Any ideas appreciated
> Murat CETINKAYA, M.Sc.
> BioNanoMaterials Group,
> Dept. of Engr. Science and Mechanics,
> The Pennsylvania State University,
> University Park, PA 16802
> office: (814) 863 9967
> web: www.personal.psu.edu/muc176
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